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2kz9

Structure of E1-69 of Yeast V-ATPase

Method: SOLUTION NMR Dmax: 106.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

V-type proton ATPase subunit E

Saccharomyces cerevisiae

UniProt P22203

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–69 Fragment：UNP residues 1-69 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；293 K；Ionic strength (raw mmCIF value) 200；Pressure AMBIENT NMR sample composition：2 mM [U-100% 13C; U-100% 15N] protein-1, 93% H2O/7% D2O | 93% H2O/7% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2KZ9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J9T Yeast V-ATPase state 1 Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 6.90 Å
3J9U Yeast V-ATPase state 2 Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 7.60 Å
3J9V Yeast V-ATPase state 3 Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside；pH 7.4；50 mM Tris-HCl, 150 mM NaCl, 0.02% w/v dodecylmaltoside
cryo-EM vitrification conditions Blot for 23 seconds before freezing；77 K；Cryogen OTHER；Blot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
Resolution 8.30 Å
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–233（233 aa）
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4DL0 Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase Deposited 2012-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–233（233 aa）
Not recorded SO4 SULFATE ION × 4 PBM TRIMETHYL LEAD ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；0.1 M Lithium Sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M Glycine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.257
4EFA Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase - second conformation Deposited 2012-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–233（233 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.1 M lithium sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M glycine , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.82 Å R-free 0.277
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Chain M 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5BW9 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-06-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain i 1–233（233 aa）
Chain k 1–233（233 aa）
Chain m 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROFLUIDIC；pH 7.5；291 K；9.5 % PEG 8k, 150mM Ammonium Sulfate, 100mM HEPES, 12.5mM MgCl2
Resolution 7.00 Å R-free 0.309
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Chain M 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5D80 Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form Deposited 2015-08-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain i 1–233（233 aa）
Chain k 1–233（233 aa）
Chain m 1–233（233 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；8.25% PEG 8000, 0.25 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.05 M Strontium Chloride
Resolution 6.20 Å R-free 0.302
5VOX Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1) Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.80 Å
5VOY Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2) Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.90 Å
5VOZ Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.60 Å
6O7V Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 Deposited 2019-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.60 Å
6O7W Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 Deposited 2019-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 7.00 Å
6O7X Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 Deposited 2019-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.70 Å
7FDA CryoEM Structure of Reconstituted V-ATPase, state1 Deposited 2021-07-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7FDB CryoEM Structures of Reconstituted V-ATPase,State2 Deposited 2021-07-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7FDC CryoEM Structures of Reconstituted V-ATPase, state3 Deposited 2021-07-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 31 PDB declaration: 31-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7FDE CryoEM Structures of Reconstituted V-ATPase, Oxr1 bound V1 Deposited 2021-07-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9COP Yeast RAVE bound to V-ATPase V1 complex Deposited 2024-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9MOY Reconstituted yeast V-ATPase bound to Rtc5p Deposited 2024-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
9NN1 Yeast V1-ATPase bound to Rtc5p Deposited 2025-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9ODU Yeast V-ATPase bound to Rtc5p, rotary state 2 Deposited 2025-04-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain G 1–233（233 aa）
Chain I 1–233（233 aa）
Chain K 1–233（233 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VATE_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–69； UniProt 1–69

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2kz9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2kz9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2kz9
Deposition date deposition_date2010-06-14
Structure title titleStructure of E1-69 of Yeast V-ATPase
Keywords keywordsV-ATPase, Subunit E, PROTON TRANSPORT; PROTON TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.60 Å
Radius of gyration Rg (electron density) rg_electron27.89 Å
Forward intensity I(0) i093525000.00
Molecular weight molecular_weight78790.0 kDa
Excluded volume excluded_volume98169 ų
Envelope volume envelope_volume35287 ų
Hydration-shell volume shell_volume11526 ų
Envelope diameter envelope_diameter108.4 Å
Shell Rg shell_rg31.16 Å
Envelope Rg envelope_rg33.44 Å
Shape Rg shape_rg27.79 Å
Total Rg total_rg28.32 Å
Total atoms total_atoms11150
Residues n_residues690
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax106.8 Å
Rg (real space) rg_real27.52 Å
Rg uncertainty (real space) rg_real_error1.75 Å
I(0) (real space) i0_real9.3530e+07
I(0) uncertainty (real space) i0_real_error1.6230e+06
Rg (reciprocal space) rg_reciprocal27.24 Å
I(0) (reciprocal space) i0_reciprocal93510000.0000
Solution quality estimate total_estimate0.6135
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary8.9 Å
Skewness Skewness skewness0.607
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36860.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.003; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.002; Smooth: 0.961
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2kz9A00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1620 —
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8. Citations (1)

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9. Files and Curves (10)